Sequence
atgc intronic sequence ATGC exonic sequence...cgagattcaggaaagccttaaaagttgagcctaggttatttgattttaagggttccttttaagttgaggattgtgactttctgtttgttgtttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
Basic information
species | Glycine max |
transcript | GLYMA14G39540.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G39540.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g49980.2 (Oryza sativa), 3'ss of exon 1
cgagattcaggaaagccttaaaagttgagc-ctaggttatttgattttaagggttccttttaagttgaggattgtgactttctgtttgttgtttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
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-aaatattagaacatacgccaatattaagtactatgcaacatgtttccttataaacatgtctagtgaaaggtttactcatgacaattatgtcctccaccagCTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT
upper sequence: GLYMA14G39540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G089454_T01 (Zea mays), 3'ss of exon 1
cgagattcaggaaagccttaaaagttgagcctaggttatttgattttaag-ggttccttttaagttgagg--attgtgacttt--ctgtttgttgtttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
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-gaaatt----agcatctgtaccagtgtgtacattttgatggcttttaagcagtgcatattgatttgtagcaattctactcatggcagtaatatttctatttcagCTTGTTTTTTAAGCAAGAAATGGAACTCTCCCTGGTTGGGTTGCAGAATGCTGGGAAGACATCGCTGGTCAATGCTGTTGCT
upper sequence: GLYMA14G39540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G089454_T04 (Zea mays), 3'ss of exon 1
cgagattcaggaaagccttaaaagttgagcctaggttatttgattttaagggttccttttaagttgagg--attgtgacttt--ctgtttgttgtttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT----------------------------------------------------------------
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--------------------------------------------------agtgcatattgatttgtagcaattctactcatggcagtaatatttctatttcagcttgttttttaagcaagaaatggaactctccctggttgggttgcagAATGCTGGGAAGACATCGCTGGTCAATGCTGTTGCTGTATGCATCAACTCAGTCAAGATACATTACCATGTTATCTGGTGTTTTGATTTTAATTCATGGC
upper sequence: GLYMA14G39540.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G37680.1 (Arabidopsis thaliana), 3'ss of exon 1
-cgagattcaggaaagccttaaaagttgagcctaggttatttgattttaagggttccttttaagttgaggattgtgactttctgtttgttgtttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
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tgttgtttttggttatacttatgtttttagtgtatagcagaatcacgttttggtaacacttagattttg-attctgtgtttgcttatatttgttgtgtcagCTTGTTTTTCAAACAAGAGATGGAGCTGTCACTCGTTGGACTTCAAAATGCTGGGAAGACTTCTCTTGTCAATGCCATTGCT
upper sequence: GLYMA14G39540.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0006g01090.t01 (Vitis vinifera), 3'ss of exon 2
cgagattcaggaaagccttaaaagttgagcctaggttatttgattttaagggttccttttaagttgaggattgtgactttct-gtttgttgtttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
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----------------gttagtatcatatttttcataacagaatatt---gatttctccttatttatgaagtcctcctcgcttaccttgtctccatatcagCTTATTTTATAAACAGGAAATGGAACTTTCTCTTATAGGCCTTCAGAATGCAGGAAAGACATCTCTTCTTAATGCCATTGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagggttccttttaagttgaggattgtgactttctgtttgttgtttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
ttttaagtt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgagattcaggaaagccttaaaagttgagcctaggttatttgattttaagggttccttttaagttgaggattgtgactttctgtttgttgtttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - gccttaa
- - - - - - - - - - - - - - - - - - - - - - - - - -gttcctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgagg